Mining Microbial Data from Existing Plant Data

[ben.sikes]

This is an effort to look at -omics data from plant space flights to parse microbial-associated molecular patterns.

[dr.richard.barker]

This gitbook page offers helpful project planning strategies and related information: Microbiome of seedling in space | Microbiome of seedling in space

[rtscott2001]

Is this going to be discussed at this upcoming Wednesday’s @MicrobesAWG mtg 1st Wednesday/mo 10a-11a PT? @daniela.bezdan @ben.sikes @dr.richard.barker

[ben.sikes]

I don’t know that we have set an agenda for the meeting @rtscott2001. @daniela.bezdan was traveling I know and we needed to cancel our last meeting. I would be happy to give an update on this project if desired. @dr.richard.barker and @Zerrin, would you be willing to go through some of your results during the meeting as well? Combined, this might take up a big chunk of the meeting so maybe I should wait to see if @daniela.bezdan already has a plan for the meeting (perhaps rescheduled from last time)?

[dr.richard.barker]

Sure, i haven’t heard from @daniela.bezdan, so always happy to adapt to her plans ( ) but note I am happy to provide a little update on @Zerrin’s analysis (&/or support Zerrin’s presentation of it if time zones allow). Note, that it’s still preliminary data and is an ongoing analysis but I think it’s about to reach a “reflection point”, so even though the final narrative is not complete I still believe it will be useful to discuss to help identify loose ends and potential solutions. Cheers, DRB

[ramkishorsah]

It’s Noted. Thank you.

Dr. Ramkishor Sah, PPHC, PhD (Ophthalmology)
Scientist-I
R.No.-104, First Floor
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Dr. R P Centre, AIIMS, Ansari Nagar
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[sharvarin04]

Is there a way to keep track of the meetings? I am in a couple of AWG groups but I don’t have a calendar of scheduled meetings.

[rtscott2001]

For the moment, all the meeting times are listed in The AWG Member Hub

But you raise a very good point. This Forum-Space does HS the ability to enable a calendar plugin. I need to read more and get that dialed in. Someone else raised the idea too @rachelrgilbert so now that I hear that from you as well, that tells me it would helps

Thank you!

[rtscott2001]

Hi @nicholas.brereton @ben.sikes - sorry I was only able to briefly join the meeting on this project yesterday.

What was the outcome?

[ben.sikes]

No worries, @rtscott2001. I was late because of a kidmergency but all good. We had a good discussion about the science and process we want to move forward with. For the Open Life Science pages here, did you have insights on how better we can organize a collaborative topic/project like this Plant-Microbe AWG one? We currently have a lot of different ways we are communicating and I’m worried about overload/loss. For example, I’m polling to schedule meetings with WhenIsGood, we’re using Google Drive for data, papers, and meeting minutes collection, @dr.richard.barker has taken a good bit of what we’ve done and put it in GitBook alongside early results. How do you think this communication tool can help in all that?

[rtscott2001]

Shoot. Yeah, as much as possible I’d suggest leveraging this thread, but also keeping the “AWG Group Member Hub” updated: Open Science Data Repository AWG Community

Microbe: https://awg.osdr.space/g/MicrobesAWG
Plant: https://awg.osdr.space/g/PlantAWG

As the AWG overall (just about 600 now), climbs towards 1000, we’re really hoping (and day by day confident), this forum-space will be the central place for general communications – BUT where GitHubs, google docs, etc can be shared.

There is a polling/voting option on meeting times here in Discourse. But I havent used it yet (calendar icon)

[adrianguzman]

Hi, I would like to be added here. Adrian Guzman

[rtscott2001]

Plant-Microbial AWG meeting

Hi all, We’d like to (finally) have a meeting to update you on progress on the Plant-Microbial AWG collaborations. The meeting will be Tuesday, April 15th at 3PM GMT/11AM EDT/8AM PDT. We’ve made good progress on the roadmap manuscript, as well as our analyses of RNA-seq data from previous plant flight experiments. We’ll provide those updates, map out where help is needed for next steps, and try to set a more regular time to meet. If you can’t make this time but want to be part of these efforts,…

[ben.sikes]

Just a quick reminder that we’ll have our update meeting this coming Tuesday, April 15th. It will be at 3PM GMT (11AM EDT, 8AM PDT). It’s on the AWG meeting calendar and here’s the Zoom link again: Launch Meeting - Zoom; PWD: 042025

And here’s the agenda:

Quick update on analysis of Arabidopsis (meta) transcriptomes using “leftovers” approach (being led by Zerrin Kim) - Richard Barker and Ben Sikes

Update on co-analysis of plant and microbe transciptomic data from prior flights by Emmanuel Gonzalez + Nick Brereton

Ongoing analyses and collection of strain genomes

Update on plant-microbe direction manuscript. Current draft is here: Loading Google Docs

Last couple sections that need content; vetting by NASA-knowledgable folks

Journal targets for submission and timeline

Authorship + how to contribute at this stage

@PlantAWG @MicrobesAWG

[Hasret]

The discussion was awesome.I would like to contribute to the article.
Could you please send me the article so that I can add some paragraphs?

Thank you for the time.

[ben.sikes]

Chart_Path-Space Plant-Microbe-Systems_12_04_25.docx

Here you go Hasret. I’ll be working this week to better combine an old version with this one but you should be able to see and comment.

[Hasret]

I would like to add some paragraphs to the manuscript.
I can only read it here. Yes?

Kind regards.
Happy Easter.